Aggregation             Aggregation of matrices list.
BalanceHiC              Compute HiC matrix-balancing.
Beaf32_Peaks.gnr        D.melanogaster Beaf-32 ChIP-seq.
BinGRanges              Bin a GRanges.
CompareToBackground     CompareToBackground
CutHiC                  Cut HiC map in chunks.
ExtractSubmatrix        Submatrix extraction.
FilterInteractions      Submatrix or Interactions filtering.
GenomicSystem           Base pairs convertion.
GetInfo                 get some basic information about your hic file
GetQuantif              Compute quantification on extracted
                        submatrices.
ggAPA                   Aggregation plot
HiC_Ctrl.cmx_lst        In situ Hi-C control.
HiC_HS.cmx_lst          In situ Hi-C heat treated.
Hue                     Hue palette.
ICEnorm                 Compute Iterative Correction.
ImportHiC               Import Hic data
IndexFeatures           Indexes GRanges on genome.
JoinHiC                 Merge HiC chunk.
MergeGRanges            Merge GRanges.
OrientateMatrix         Matrix orientation
OverExpectedHiC         Genomic distance bias correction.
PlotAPA                 Draw aggregation plot.
plotMultiAPA            Draw aggregation plots for interactions with
                        different distances.
PrepareMtxList          Prepare matrices list for further analysis.
preparePlotgardener     preparePlotgardener
SearchPairs             Creates pairs from genomic index.
SeqEnds                 Get all sequences lengths.
StrToGRanges            Convert String to GRanges.
SwitchMatrix            Change values of HiC map.
TADs_Domains.gnr        D.melanogaster TADs.
TSS_Peaks.gnr           D.melanogaster Transcription starting sites.
VCnorm                  Compute Vanilla Count Correction.
viridis                 viridis palette.
YlGnBu                  YlGnBu palette.
YlOrRd                  YlOrRd palette.
